Handle `uintptr_t`s better in JNI bindings

This fixes bugs building for 32-bit platforms as the JNI functions
would expect `uintptr_t`s (32-bit) but Java expects a long (64-bit).
We can't just replace them all with int64_ts as we need to have
`uintptr_t`s still in _jcalls functions which we pass function
pointers to C.